[phenixbb] PHENIX refine: detached sidechain atoms

[Oliver King]

Hi All,

I've noticed that when refining a model in phenix.refine using a PDB 
file from Refmac, the sidechain atoms of certain residues become 
detached from the rest of the molecule and appear to float on their own, 
at least when viewing in Coot. I think this is down to the format of the 
PDB file. For example the atoms of a Leu residue from a phenix.refine 
file which displays well is of the form:

ATOM      1  N   LEU A   8      50.022 -34.247  -5.817  1.00 
58.12           N
ATOM      2  CA  LEU A   8      49.788 -34.905  -4.539  1.00 
55.84           C
ATOM      3  C   LEU A   8      48.339 -35.358  -4.348  1.00 
60.39           C
ATOM      4  O   LEU A   8      48.008 -36.016  -3.360  1.00 
68.40           O
ATOM      5  CB  LEU A   8      50.219 -34.011  -3.373  1.00 
57.98           C
ATOM      6  CG  LEU A   8      51.690 -34.126  -2.975  1.00 
65.66           C
ATOM      7  CD1 LEU A   8      52.014 -33.170  -1.836  1.00 
59.99           C
ATOM      8  CD2 LEU A   8      52.020 -35.566  -2.594  1.00 
68.57           C

where as from a Refmac PDB which also behaves well, it is of the form:

ATOM      1  N   LEU A   8      50.453 -35.722  -5.617  1.00 
20.00           N
ATOM      2  CA  LEU A   8      49.649 -35.131  -4.482  1.00 
20.00           C
ATOM      3  CB  LEU A   8      50.190 -33.735  -4.147  1.00 
20.00           C
ATOM      4  CG  LEU A   8      51.461 -33.755  -3.275  1.00 
20.00           C
ATOM      5  CD1 LEU A   8      52.556 -32.768  -3.741  1.00 
20.00           C
ATOM      6  CD2 LEU A   8      51.082 -33.546  -1.799  1.00 
20.00           C
ATOM      7  C   LEU A   8      48.166 -35.063  -4.824  1.00 
20.00           C
ATOM      8  O   LEU A   8      47.822 -34.257  -5.568  1.00 
20.00           O

but after refinement in phenix it becomes

ATOM      1  N   LEU A   8      50.734 -35.936  -5.935  1.00 
54.45           N
ATOM      2  CA  LEU A   8      49.846 -35.185  -4.892  1.00 
51.89           C
ATOM      3  CB  LEU A   8      50.377 -33.761  -4.516  1.00 
51.22           C
ATOM      4  CG  LEU A   8      51.550 -33.730  -3.431  1.00 
59.27           C
ATOM      5  CD1 LEU A   8      52.457 -32.407  -3.635  1.00 
60.88           C
ATOM      6  CD2 LEU A   8      51.120 -34.090  -1.879  1.00 
55.50           C
ATOM      7  C   LEU A   8      48.268 -35.042  -5.221  1.00 
47.92           C
ATOM      8  O   LEU A   8      47.989 -34.282  -6.195  1.00 
47.32           O

and the CD2 atom is now too far away to be part of the residue in Coot

Is there an easy way to convert a PDB from Refmac into one which will 
behave itself when put through phenix.refine? I've tried using 
phenix.pdb_tools and also putting the model through Molprobity and 
hoping that that the output would be corrected.

Thanks,

Olly King